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Sample GSM2788284 Query DataSets for GSM2788284
Status Public on Jul 19, 2018
Title iRx_noDoxJQ1_RNAseq_rep2
Sample type SRA
 
Source name un-induced plus JQ1 treated RNA-seq
Organism Mus musculus
Characteristics mouse strain: 129P2/OlaHsd
cell type: haemogenic endothelium (HE) cells
genotype: un-induced plus JQ1 treated
Extracted molecule total RNA
Extraction protocol RNA was extracted from cells using TRIzol (Invitrogen) according to manufacturer’s instructions. First-strand cDNA synthesis was carried out using Superscript II (Invitrogen) and Oligo dT (Invitrogen) according to manufacturer’s instructions. RNA was DNase treated using Turbo DNase (Ambion) and a further clean-up step was performed using the RNA Nucleospin kit (Macherey-Nagel) according to manufacturer’s instructions. Real-time PCR was carried out using Applied Biosystems SYBR green master mix (Thermo Fisher) with 5 μl of diluted cDNA and 0.25 μM forward and reverse primers per 10 μl reaction on an ABI 7900HT machine. Analysis was carried out on samples measured in duplicate.
RNA-seq libraries were prepared using the Tru-seq Stranded Total RNA kit (Illumina), according to manufacturer’s instructions. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq® 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina, FC-404-2002) at the Genomics Birmingham sequencing facility.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Quality of reads was verified using FASTQC analysis
RNA-Seq reads were aligned to the mm10 mouse genome build using STAR.
Separate density files for the positive and negative strand were generated for RNA-seq data and uploaded to the UCSC genome browser
Fragments per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
 
Submission date Sep 20, 2017
Last update date May 15, 2019
Contact name Salam Adli Assi
E-mail(s) s.a.assi@bham.ac.uk
Organization name University of Birmingham
Department Institute for Cancer and Genomic Sciences
Street address IBR
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL17021
Series (2)
GSE104044 System-wide Dissection of the Transcriptional Response to RUNX1 During Hematopoietic Specification [RNA-seq]
GSE104046 The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification
Relations
BioSample SAMN07674696
SRA SRX3200425

Supplementary file Size Download File type/resource
GSM2788284_iRx_noDoxJQ1_RNAseq_rep2.bedgraph.gz 214.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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